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. 2020 Jan 27;5(1):887–888. doi: 10.1080/23802359.2020.1718027

The complete chloroplast genome of Epimedium brevicornu (Berberidaceae), a traditional Chinese medicinal herb

Yu Yao a,*, Xiang Liu a,b,*, Qianru Yang a, Yanjiao Luo c, Cheng Zhang a, Chaoqun Xu a, Fengmei Suo a, Guoan Shen a,✉, Baolin Guo a,✉
PMCID: PMC7748714  PMID: 33366798

Abstract

Epimedii Folium has been used as a common traditional Chinese medicine for more than 2000 years in China. In this study, we assembled the complete chloroplast (cp) genome of Epimedium brevicornu. The whole cp genome of E. brevicornu is 158,658 bp in length, comprising a pair of inverted repeat (IR) regions (27,699 bp) separated by a large single copy (LSC) region (86,558 bp) and a small single copy (SSC) region (16,702bp). The E. brevicornu cp genome contains 129 genes, of which 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis shows that E. brevicornu is closely clustered with E. wushanense, E. lishihchenii, and E. sagittatum. The published E. brevicornu chloroplast genome will provide useful information for the phylogenetic and evolutionary study on Epimedium family of Berberidaceae.

Keywords: Chloroplast genome, Epimedium brevicornu, Berberidaceae

Epimedii Folium, also known as Yinyanghuo, has been widely used as Traditional Chinese Medicines (TCM) for more than two thousand years in China. The leaves of some plant species in the Epimedium family have beneficial effects on human beings and animals as tonic, aphrodisiac and antirheumatics in curing sexual dysfunction and osteoporosis (Ma et al. 2011). Epimedium brevicornu Maxim. and other three species of the genus Epimedium L. are used as medicinal materials of Epimedii Folium according to Chinese Pharmacopoeia Commission’s (2015) suggestion. Epimedium family is taxonomically and phylogenetically regarded as one of the most challengingly difficult taxa in plant kingdom (Zhang et al. 2016). Since Epimedii Folium were mainly from wild resources in the market, the species confusion of Epimedium resulted in uncontrollable quality and unstable curative effects of medicinal materials (De Smet et al. 2012). The chloroplast genomes are conservative, thus it is more efficient to distinguish closely related plants at the species and population levels by using the chloroplast genome than chromosome genomic DNA regions (Li et al. 2015). Therefore, we reported the complete chloroplast genome sequence of E. brevicornu in the present study.

The total genomic DNA was extracted from the fresh leaves of E. brevicornu with a modified CTAB method (Doyle and Doyle 1987). The voucher sample (18,042) were cultivated in the Lixian County of Gansu Province, China (N34°06′, E105°32′) and deposited at the Herbarium of the Institute of Medicinal Plant (IMPLAD), Beijing, China. The 500 bp shotgun library construction was prepared from total DNA. The sequencing was performed using Illumina Novaseq PE150 platform. The filtered reads were assembled using the program GetOrganelle (Jin et al. 2018) with the reference chloroplast genome of E. acuminatum (GenBank accession number: NC_029941), the chloroplast genome was annotated through the online program CPGAVAS2 (Shi et al. 2019) and GeSeq (Tillich et al. 2017), followed by manual correction. The annotated chloroplast genome sequence has been deposited into GenBank (Accession number MN803415). The phylogenetic tree was generated based on the shared protein-coding genes among E. Brevicornu and other 20 species retrieved from the NCBI GenBank database. MAFFT v7 (Katoh et al. 2017) was used to align the sequences, and a maximum likelihood tree was generated by using RAxML v8.2.10 (Stamatakis 2014), with Sinofranchetia chinensis as the outgroup.

The complete chloroplast genome size of E. brevicornu is 158,658 bp in length, containing a large single-copy (LSC) region of 86,559 bp, a small single-copy (SSC) region of 16,703 bp, and two inverted repeat (IRa and IRb) regions of 27,698 bp. The total GC content of complete chloroplast genome, LSC, SSC, and IR regions is 38.85%, 37.29%, 33.01%, and 43.06%, respectively. In total, 129 genes were annotated, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. One trnQ-UUG gene is duplicated in the LSC regions. Six protein-coding genes (rpl2, rp123, ndhB, rps7, rps19, and ycf2), seven tRNA genes (trnI-CAU, trnL-CAA, trnV-GAC, trnI-GAU, trnA-UGC, trnR-ACG, and trnN-GUU), and four rRNA genes (rrn16, rrn23, rrn4.5, and rrn5) are duplicated in the IR regions. In these genes, 15 genes (six tRNA genes and nine protein-coding genes) contain one intron, and three genes (ycf3, clpP, and rps12) contain a couple of introns. The 5′ end and 3′ end of rps12 gene is duplicated in the LSC regions and IR regions, respectively. The rps12 gene is trans-spliced.

Phylogenetic analysis shows that E. brevicornuis is closely clustered with E. wushanense, E. lishihchenii, and E. sagittatum (Figure 1). The published E. brevicornu chloroplast genome will provide useful information for the phylogenetic and evolutionary study on Epimedium family of Berberidaceae.

Figure 1.

Figure 1.

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ML phylogenetic tree was constructed based on the shared protein-coding genes shared between the 20 species.

Funding Statement

This work was supported by the CAMS Innovation Fund for Medical Sciences [CIFMS] [2017-12M-3-013], the National Nature Science Foundation of China [81473302], the Chongqing Science and Technology Bureau [cstc2018jcyjAX0316, cc-cstc-CA-19-2], and the Traditional Chinese Medicine Science and the Technology Projects of Chongqing Health and Family Planning Commission [ZY201802117].

Disclosure statement

No potential conflict of interest was reported by the authors.

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